ArticleNucleic acids research2018
Single-molecule DNA unzipping reveals asymmetric modulation of a transcription factor by its binding site sequence and context.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 28 citations in OpenAlex.
- Optimising DNA origami assembly by reducing off-target interactions.Nature communications · 2026Article
- Chromatin boundary permeability is controlled by CTCF conformational ensembles.bioRxiv : the preprint server for biology · 2026Article
- Intrinsically disordered regions facilitate target search to drive promoter selectivity by a yeast transcription factor.Nature communications · 2025Article
- Article
- Mechanisms for DNA Interplay in Eukaryotic Transcription Factors.Annual review of biophysics · 2025Review
- DNA calorimetric force spectroscopy at single base pair resolution.Nature communications · 2025Article
- Optical tweezers in biomedical research - progress and techniques.Journal of medicine and life · 2024Review
- An i-motif-regulated enhancer, eRNA and adjacent lncRNA affect Lhb expression through distinct mechanisms in a sex-specific context.Cellular and molecular life sciences : CMLS · 2024Article
- Structural dynamics in chromatin unraveling by pioneer transcription factors.Biophysical reviews · 2024Review
- Investigation of metal ion binding biomolecules one molecule at a time.Frontiers in chemistry · 2024Review
- Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation.Nucleic acids research · 2021Article
- Dynamics and inhibition of MLL1 CXXC domain on DNA revealed by single-molecule quantification.Biophysical journal · 2021Article
- The complex architecture of p53 binding sites.Nucleic acids research · 2021Article
- Unravelling the role of epigenetics in reproductive adaptations to early-life environment.Nature reviews. Endocrinology · 2020Review
- How affinity of the ELT-2 GATA factor binding toDevelopment (Cambridge, England) · 2020Article
- Model-driven generation of artificial yeast promoters.Nature communications · 2020Article
- The base pair-scale diffusion of nucleosomes modulates binding of transcription factors.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Article
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Most functional transcription factor (TF) binding sites deviate from their 'consensus' recognition motif, although their sites and flanking sequences are often conserved across species. Here, we used single-molecule DNA unzipping with optical tweezers to study how Egr-1, a TF harboring three zinc fingers (ZF1, ZF2 and ZF3), is modulated by the sequence and context of its functional sites in the Lhb gene promoter. We find that both the core 9 bp bound to Egr-1 in each of the sites, and the base pairs flanking them, modulate the affinity and structure of the protein-DNA complex. The effect of the flanking sequences is asymmetric, with a stronger effect for the sequence flanking ZF3. Characterization of the dissociation time of Egr-1 revealed that a local, mechanical perturbation of the interactions of ZF3 destabilizes the complex more effectively than a perturbation of the ZF1 interactions. Our results reveal a novel role for ZF3 in the interaction of Egr-1 with other proteins and the DNA, providing insight on the regulation of Lhb and other genes by Egr-1. Moreover, our findings reveal the potential of small changes in DNA sequence to alter transcriptional regulation, and may shed light on the organization of regulatory elements at promoters.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.